Visualization of phylogenetic trees and forests
I am interested in the visualization of data in evolutionary biology, in particular (very) large phylogenetic trees and phylogenetic forests of gene trees.
Recently, I developed Lifemap (http://lifemap.univ-lyon1.fr), an online tool to explore the whole Tree of Life.

In collaboration with Stéphane Dray, we are currently offering a 6-month internship for a Master student to work on developing a tool to visualize large trees in R, using the Shiny library. The detailed description of the project is available below.

Horizontal Gene Transfer and the detection of extinct and unknown diversity

HGT is frequent in prokaryotes. Extent species certainly acquired genes by HGT from species that are nowadays extinct or still unknown. One of the objectives of this project is to detect such genes and use them to reconstruct extinct and unknown diversity.

Understanding the success of the few "scandalous" ancient asexual species (Bdelloid rotifers, Darwinulidae and Oribatid mites) is a key step in answering "the queen of the questions in evolutionary biology" (Bell, 1982) : why are most eukaryotic species sexual ?
An important observation made on the Bdelloid rotifers is that a large fraction of their genes come from distant species through HGT (plants, bacteria, fungi). I explore short-distance (up to within-species) events of HGT and recombination using RADseq data.